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First Aid Biochem Flashcards

1
Q

Histones are rich in what amino acids?

A

lysine and arginine

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2
Q

How does H1 stabilize the chromatin fiber?

A

H1 binds to the nucleosome and to “linker DNA”

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3
Q

What proteins make up a nucleosome?

A

(H2A, H2B, H3, H4) x2

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4
Q

What are Barr bodies?

A

inactive X chromosomes; heterochromatin

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5
Q

What allows mismatch repair enzymes to distinguish between old and new strands in prokaryotes?

What happens at CpG islands?

A

template strand cytosine and adenine are methylated in DNA replication

DNA methylation at CpG islands represses transcription

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6
Q

What does histone methylation cause?

A

usually reversibly represses DNA transcription, but can activate it in some cases depending on methylation location

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7
Q

What relaxes DNA coiling, allowing for transcription?

A

histone acetylation

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8
Q

What drugs disrupt pyrimidine synthesis?

A

leflunomide, methotrexate, TMP, pyrimethamine

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9
Q

de novo pyrimidine base production requires what amino acid?

A

aspartate

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10
Q

what does leflunomide inhibit?

A

pyrimidine synthesis by inhibiting dihydroorotate dehydrogenase

(creating orotic acid from carbamoyl phosphate and aspartate)

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11
Q

methotrexate, trimethoprim, and pyrimethamine all do what to inhibit pyrimidine synthesis

A

inhibit dihydrofolate reductase

(decrease deoxythymidine monophosphate (dTMP) in humans, bacteria, and protozoa, respectively)

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12
Q

what forms 5-F-dUMP? what does this do?

A

5-fluorouracil (5-FU) inhibits pyrimidine synthesis by forming 5-F-dUMP, which inhibits thymidylate synthase

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13
Q

What drugs disrupt purine synthesis?

A

6-MP and mycophenolate and ribavirin

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14
Q

What is the prodrug of 6-MP? What do they both do?

A

azathioprine

inhibit purine synthesis by inhibiting PRPP from becoming IMP

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15
Q

how does mycophenolate and ribavirin work?

A

inhibit ionosine monophosphate dehydrogenase from becoming GMP

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16
Q

What drug inhibits purine and pyrimidine synthesis? How does this work?

A

hydroxyurea - inhibits ribonucleotide reductase

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17
Q

what does de novo purine base production require?

A

aspartate, glycine, glutamine, and THF

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18
Q

deamination of cytosine makes

A

uracil

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19
Q

deamination of adenine makes

A

guanine

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20
Q

methylation of uracil makes

A

thymine

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21
Q

One of the major causes of autosomal recessive SCID, this is required for degradation of adenosine and deoxyadenosine…

What happens in deficiency of this enzyme?

A

adenosine deaminase deficiency

increased dATP leads to toxicity in lymphocytes

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22
Q

In Lesch- Nyhan syndrome, there is defective purine salvage due to…

what does this normally do?

ssx?

A

due to absent HGPRT

converts hypoxanthine to IMP and guanine to GMP

exess uric acid production and de novo purine synthesis – hyperuricemia, gout, aggression/self-mutilation, retardation, dystonia

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23
Q

“orange sand” in diaper is actually…

A

sodium urate crystals, a sign of Lesch-Nyhan syndrome

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24
Q

What amino acids are specified by only one codon?

A

methionine - AUG

tryptophan - UGG

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25
Q

Origin of replication in eukaryotes and prokaryotes differs because…

A

in eukaryotes there are multiple origins of replication

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26
Q

What is the Y shaped region along DNA template?

what happens here?

A

replication fork

leading and lagging strands are synthesized

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27
Q

what prevents strands from reannealing?

A

single-stranded binding proteins (SSBPs)

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28
Q

what creates a single or double strand break in the helix to add or remove supercoils?

A

DNA topoisomerases

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29
Q

What drugs inhibit eukaryotic topoisomerase I?

A

irinotecan and topotecan

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30
Q

what drugs inhibit eukaryotic topoisomerase II?

A

etoposide and teniposide

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31
Q

what drugs inhibit prokaryotic topoisomerase II (DNA gyrase) and topoisomerase IV?

A

fluoroquinolones

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32
Q

Primase makes an RNA primer on which …

A

DNA polymerase III can initiate replication

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33
Q

In prokaryotes only, this enzyme will elongate the leading strand by adding deoxynucleotides to the 3’ end. It also elongates the lagging strand until it reaches primer of preceding fragment.

A

DNA polymerase III

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34
Q

What kind of synthesis and exonuclease power does DNA polymerase III have?

A

has 5’ to 3’ synthesis and proofreads with 3’-5’ exonucleases

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35
Q

What is the modification in most drugs that block DNA replication?

A

modified 3’ OH, preventing the addition of the next nucleotide, chain termination

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36
Q

What enzyme is prokayotic only and degrades the RNA primer to replace it with DNA? How does it do this?

A

DNA polymerase I

same function as DNA polymerase III, also exises RNA primer with 5’ to 3’ exonuclease

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37
Q

What enzyme catalyzes the formation of a phosphodiester bond within a strand of dsDNA?

what is this doing?

A

DNA ligase

joins Okazaki fragments

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38
Q

in eukaryotes only, this enzyme is an RNA-dependent DNA polymerase that adds DNA to 3’ ends of chromosomes to avoid loss of genetic material with every duplication

when is this an issue?

A

telomerase

often dysregulated in cancer cells allowing unlimited replication

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39
Q

transition v transversion in DNA mutation

A

transition is purine to purine or pyrimidine to pyrimidine

transversion is purine to pyrimidine or vice versa

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40
Q

nucleotide substitution resulting in changed amino acid

A

missense

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41
Q

What ares two disease examples with frameshift mutations?

A

Duchenne MD and Tay-Sachs

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42
Q

What is the purpose of the lac operon?

What is the mechanism of this shift?

A
  • genetic response to an environmental change
  • glucose preffered metabolis substrate for E. coli, but when it is absent and lactose is available, the lac operon is activated to switch to lactose metabolism
  • low glucose
    • increase adenylate cyclase activity
      • increase generation of cAMP from ATP
        • activation of catabolite activator protein (CAP)
          • increase transcription
  • high lactose
    • unbinds repressor protein from repressor/operator site
      • increase transcription
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43
Q

What repairs bulky-helix distorting lesions? What phase of the cell cycle does this happen in? When is this defective?

A

nucleotide excision repair

G1 phase

defective in xeroderma pigmentosum

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44
Q

How does base excision repair work? When does it occur?

A
  • base-specific Glycosylase removes altered base and creates AP (apurinic or apyrimidinic) site
  • one or more nucleotides removed by AP-Endonuclease
    • cleaves at 5’ end
  • Lyase cleaves at 3’ end
  • DNA polymerase-B fills the gap
  • DNA ligase seals it

occurs through cell cycle

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45
Q

When does mismatch repair occur in the cell cycle?

A

G2 phase of cell cycle

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46
Q

What brings together 2 ends of DNA fragments to repair double stranded breaks?

When is this defective?

A

nonhomologous end joining

defective in ataxia telangiectasia, breast/ovarian cancers with BRCA1 mutation, and Fanconi anemia

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47
Q

What binds at the DNA promoter regions?

A

RNA polymerase II and multiple other transcription factors

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48
Q

RNA polymerases make what in eukaryotes?

A
  • RNA polymerase I makes rRNA (most numerous - rampant)
  • RNA polymerase II makes mRNA (largest - massive)
    • mRNA read 5’ to 3’
    • opens DNA at promoter site
  • RNA polymerase III makes 5sRNA, tRNA (smallest RNA, tiny)

no proofreading function, but can initiate chains

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49
Q

What drug inhibits DNA-dependent RNA polymerase in prokaryotes?

A

rifampin

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50
Q

What is found in death cap mushrooms and why is this toxic?

A

alpha-amanitin - found in Amanita phalloides

inhibits RN polymerase II

severe hepatotoxicity

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51
Q

What does RNA start as and then how is it modified in the nucleus?

A

hnRNA (heterogenous nuclear)

capping 5’ end, polyadenylation of 3’ end, splicing out of introns => mRNA

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52
Q

What happens to mRNA in the cytosol?

A

translated

quality control occurs at cytoplasmic processing bodies called P bodies which contain exonucleases, decapping enzymes, and microRNAs

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53
Q

Where can mRNA be stored for future translation?

A

P bodies in the cytoplasm

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54
Q

What forms a spliceosome?

A

primary transcript combines with small nuclear ribonucleotides (snRNPs) and other proteins to form spliceosome

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55
Q

Antibodies to splicesomal snRNPs are aka ….

and are highly specific for…

A

anti-Smith abs; SLE

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56
Q

Anti-U1 RNP abs are high associated with …

A

mixed connective tissue disease

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57
Q

What posttranscriptionally regulate gene expression by targeting the 3’ untranslated region of specific mRNAs for degradation or translational repression?

A

microRNAs

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58
Q

What are the arms of tRNA for?

A
  • CCA at 3’ end along with a high percentage of chemically modified bases - covalently binds amino acid
  • T arm has TŶC (ribothymidine, pseudouridine, cytidine) tethers tRNA molecule to ribosome
  • D arm contains dihydrouridine residues - detects the tRNA by aminoacyl-tRNA synthetase
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59
Q

What is responsible for accuracy of amino acid selection?

A

aminoacyl-tRNA synthetase and binding of charged tRNA to the codon

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60
Q

protein synthesis initiation

A

initiated by GTP hydrolysis; initiation factors (eukaryotic IFs) help assemble the 40S ribosomal subunit with the initiator tRNA and are released when the mRNA and the ribosomal 60S subunit assemble with the complex

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61
Q

Protein synthesis elongation stage

A
  1. aminoacyl-tRNA binds to A site (except for initiator methionine
  2. rRNA (ribozyme) catalyzes peptide bond formation, transfers growing polypeptide to amino acid in A site
  3. ribosome advances 3 nucleotides toward 3’ end of mRNA, moving peptidyl tRNA to P site (translocation)
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62
Q

Summary of sites in protein synthesis

A

A site: incoming aminoacyl-tRNA

P site: accomodoates growing peptides

E site: holds empty tRNA as it exits

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63
Q

Protein synthesis termination

A

stop codon is recognized by release factor and completed peptide is released from the ribosome

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64
Q

Posttranslational modifications include…/

A

trimming - remove N or C terminal peptides from zymogen to generate mature peptides

covalent alterations - phosphorylation, glycosylation, hydroxylation, methlyation, acetylation, and ubiquitination

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65
Q

intracellular protein involved inf acilitating and/or maintaining protein folding

example?

A

chaperone protein

eg in yeast, heat shock proteins - HSP60 - expressed at high temps to prevent protein denaturing/misfolding

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66
Q

What mediates check points in the cell cycle?

A

cyclins, CDKs - cyclin dependent kinases, and tumor suppressors

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67
Q

what phosphorylates other proteins to coordinate cell cycle progression?

A

cyclin-CDK complexes

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68
Q

how are CDKs inhibited?

A

p53 induces p21 to inhibit CDK

hypophosphorylation (activation) of Rb

inhibition of G1-S progression

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69
Q

What types of cells remain in G0 and regenerate from stem cells? What are examples of these cells?

A

permanent cell type

neurons, skeletal and cardiac muscle, RBCs

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70
Q

What type of cells enter G1 from G0 when stimulated?

What are examples of these cells?

A

stable (quiescent) cells

hepatocytes and lymphocytes

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71
Q

What cells never go to G0, but divide rapidly with a short G1?

What are examples of these cells?

A

labile type cells

bone marrow, gut epithelium, skin, hair follicles, germ cells

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72
Q

How does the Golgi modify some amino acids?

A
  • modifies N-oligosaccharides on asparagine
  • adds O-oligosaccharides on serine and threonine
  • adds mannose-6-phosphate to proteins for trafficking to lysosomes
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73
Q

what are sorting centers for material from outside the cell or from the Golgi, sending it to lysosomes for destruction or back to the membrane/Golgi for further use?

A

endosomes

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74
Q

What happens in I-cell disease?

A

inclusion cell disease/mucolipidosis type II

  • inherited lysosomal storage disorder
  • defect in N-acetylglucosaminyl-1-phosphotransferase
    • failure of Golgi to phosphorylate mannose residues on glycoproteins
      • proteins are secreted extracellularly rather than delivered to lysosomes
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75
Q

How does I cell disease present?

A

coarse facial features, clouded corneas, restricted joint movement, and high plasma levels of lysosomal enzymes

often fatal in childhood

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76
Q

abundant, cytosolic ribonucleoprotein that traffics proteins from the ribosome to the RER;

what happens if this is absent or dysfunctional?

A

signal recognition particle (SRP)

proteins accumulate in the cytosol

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77
Q

What are vesicular trafficking proteins?

A
  • COP1: Golgi to Golgi (retrograde); cis-Golgi to ER
  • COPII: ER to cis-Golgi (anterograde)
  • Clathrin: trans-Golgi to lysosomes; plasma membrane to endosomes (receptor mediated endocytosis) eg LDL receptor activity
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78
Q

what organelle is involved in catabolism of very long chain fatty acids, branched-chain fatty acids, amino acids and ethanol?

A

peroxisome

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79
Q

What are some examples of peroxisomal disease and presentation?

A
  • deficits in synthesis of plasmalogens, important phospholipids in myelin
  • Zellwger syndrome
    • hypotonia, hepatomegaly, early death
  • Refsum disease
    • scaly skin, ataxia, cataracts/night blindness, shortening of fourth toe, epiphyseal dysplasia
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80
Q

what degrades ubiquitin-tagged proteins?

A

proteasome

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81
Q

Staining for vimentin will identify what?

A

mesenchymal tissue

mesenchymal tumors (sarcoma), but also endometrial carcinoma, RCC, meningioma

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82
Q

Staining for desmin will identify what kind of tumor?

A

muscle tumors like rhabdomyosarcoma

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83
Q

Staining for GFAP will identify what tumor types?

A

neuroglia - astrocytomas and glioblastomas

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84
Q

How is cilia structure arranged?

A

9 doublets and 2 singlets of microtubules

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85
Q

In the Na-K pump, what inhibits binding to the K+ site?

A

ouabain

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86
Q

Where is each type of collagen found?

A
  1. MC - bone, skin, tendon, dentin, fascia, cornea, late wound repair
  2. cartilage (including hyaline), vitreous body, nucleus pulposus
  3. reticulin - skin, blood vessels, uterus, fetal tissue, granulation tissue
  4. basement membrane, basal lamina, lens
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87
Q

What are steps of collagen synthesis?

A
  1. Pro alpha chain backbone (Gly-X-Y)
  2. hydroxylation of proline and lysine (requires vit C)
  3. glycosylation (triple helix formation)
  4. exocytosis
  5. cleavage of procollagen C- and N- terminals creating insoluble tropocollagen
  6. formation of cross-links (stabilzed by lysyl oxidase)
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88
Q

Osteogenesis imperfecta is MC a/w what gene defects?

A

COL1A1 and COL1A2

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89
Q

What gene defects are a/w Ehlers Danlos?

A

Classic type is collagen V - COL5A1, COL5A2

Vascular type deficient type III collagen

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90
Q

X linked recessive CT disorder caused by impaired copper absorption and transport due to defective …. protein (ATP7A)

dx?

what does this result in?

A

Menkes disease

leads to decreased activity of lysyl oxidase (copper is a necessary cofactor)

results in brittle, “kinky” hair, growth retardation, and hypotonia

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91
Q

wrinkles of aging are caused by

A

decreased collagen and elastin production

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92
Q

elastin is rich in

A

nonhydroxylated proline, glycine, and lysine residues

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93
Q

what gives elastin its elastic properties?

A

cross-linking takes place extracellularly

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94
Q

What is the gene defect in Marfan syndrome?

A

FBN1 gene mutation on chromosome 15 results in defective fibrillin, a glycoprotein that forms a sheath around elastin

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95
Q

What are the steps of PCR?

A
  1. denaturation - heated into separate strands
  2. annealing - during cooling, excess DNA primers anneal to a specific sequence on each strand to be amplified
  3. elongation - heat-stable DNA polymerase replicates the DNA sequence following each primer
96
Q

What is a confirmatory test for HIV after a positive ELISA?

A

Western blot

97
Q

What kind of lab test is used for work up of hematologic abnormalities and immunodeficiencies?

how is data plotted?

A

flow cytometry - assess size, granularity, and protein expression (immunophenotype) of individual cells in a sample

plotted as histogram or scatter plot

98
Q

when thousands of nucleic acid sequences are arranged in grids on glass or silicone this is an example of …

what can this detect?

A

microarray

detect single nucleotide polymorphisms (SNPs) and copy number variations (CNVs) for a variety of applications including genotyping, clinical genetic testing, forensic analysis, cancer mutations, and genetic linkage analysis

99
Q

what is an immunologic test used to detect the presence of either a specific ag or ab?

A

enzyme-linked immunosorbent assay (ELISA)

100
Q

Describe the karotyping process

A

metaphase chromosomes are stained, ordered, and numbered according to morphology, size, arm-length ratio, and banding pattern

101
Q

what is FISH lab work used for?

A

specific localization of genes and direct visualization of chromosomal anomalies at the molecular level

102
Q

What are the steps of cloning?

A
  1. isolate eukaryotic mRNA
  2. expose mRNA to RT to produce cDNA (lacks introns)
  3. insert cDNA fragments into bacterial plasmids containing abx resistance genes
  4. transform recombinant plasmid into bacteria
  5. surviving bacteria on abx medium produce cloned DNA (copies of cDNA)
103
Q

Cre-lox system

A

can inducibly manipulate genes at specific developmental points

104
Q

dsRNA is synthesized that is complementary to the mRNA sequence of interest; when transfected into human cells, dsRNA separates and promotes degradation of target mRNA

what is this called and what will this do?

A

RNA interference

knocking down gene expression

105
Q

tendency for certain alleles at 2 linked lock to occur together more or less often than expected by chance; measured in population, not family

A

linkage disequilibrium

106
Q

pt inherits or develops a mutation in a tumor suppressor gene, the complementary allele must be deleted/mutated before cancer develops

A

loss of heterozygosity (2 hit hypothesis)

107
Q

mutation arises from mitotic errors after fertilization and propagates through multiple tissues or organs

A

somatic mosaicisim

108
Q

mutations at different loci can produce a similar phenotype

A

locus heterogneity

109
Q

different mutations in the same locus produce the same phenotype

A

allelic heterogeneity

110
Q

presence of both normal and mutated mtDNA, resulting in variable expression in mitochondrially inherited disease

A

heteroplasmy

111
Q

offspring receives 2 copies of a chromosome from 1 parent and no copies from the other parent

A

uniparental disomy (euploid)

112
Q

What is the difference between heterodisomy and isodoisomy?

A

heterodisomy indicates a meiosis I error

isodisomy indicates a meisosis II error or postzygotic chromosomal duplication of one pair of chronosomes, and loss of the other of the original pair

113
Q

What am I considering when I find a recessive disorder when only one parent is a carrier?

A

uniparental disomy

114
Q

hardy-weinberg law assumptions

A
  1. no mutation occurring at the locus
  2. natural selection is not occurring
  3. completely random mating
  4. no net migration
115
Q

due to defects in structural genes; many generations, males and females affected

A

autosomal dominant

116
Q

often due to enzyme deficiencies; usually only seen in one generation

A

autosomal recessive

117
Q

sons of heterozygous mothers have 50% chance of being affected;

A

x linked recessive

118
Q

transmitted through both parents; mothers transmit to 50% of daughters and sons; fathers transmit to all daughters but no sons

A

X linked dominant

119
Q

transmitted only through the mother; all offspring of affected females may show signs of disease

A

mitochondrial inheritance

120
Q

female carriers variably affected depending on the pattern of inactivation of the X chromosome carrying the mutant v normal gene

A

lyonization

121
Q

X linked recessive disorders

A

Oblivious Female Will Often Give Her Boys Her x-Linked Disorders

  • Ornithine transcarbamylase deficiency
  • Fabry disease
  • Wiskott-Aldrich syndrome
  • Ocular albinism
  • G6pD deficiency
  • Hunter syndrome
  • Bruton agammaglobulinemia
  • Hemophilia A and B
  • Lesch-Nyhan syndrome
  • Duchenne and Becker MD
122
Q

autosomal dominant; CTG trinucleotide repeat expansion in the DMPK gene

dx?

what is abnormally expressed?

ssx?

A

Myotonic type 1 Muscular Dystrophy

abnormal expression of myotonin protein kinase

myotonia, muscle wasting, cataracts, testicular atrophy, frontal balding, arrhythmia

123
Q

trinucleotide repeat in FMR1 gene (CGG) - dx?

inheritance pattern?

what does this repeat cause?

A

Fragile X syndrome

X linked dominant

hypermethylation and decreased expressivity

124
Q

What are 4 trinucleotide repeat expansion diseases?

A

Huntington disease (CAG)

Myotonic dystrophy (CTG)

Fragile X syndrome (CGG)

Friedreich Ataxia (GAA)

125
Q

What does the first trimester US show for Down Syndrome?

A

increased nuchal translucency and hypoplastic nasal bone; decreased serum PAPP-A, increased beta-hCG

126
Q

What does second trimester quad screen for Down Syndrome show?

A

decreased AFP, increased b-hCG, decreased estriol, increased inhibin A

127
Q

What screening tests do you find positive with trisomy 18?

A

PAPP-A and free b-hCG are decreased in first tri

quad screen shows decreased AFP, decreased b-hCG, decreased estriol and normal or decreased inhibin A

128
Q

chromosome 3

A

von Hippel Lindau, RCC

129
Q

chromosome 4

A

ADPKD (PKD2), achondroplasia, Huntingtons

130
Q

chromosome 5

A

cri-du-chat, FAP

131
Q

chromosome 6

A

hemochromatosis (HFE)

132
Q

chromosome 7

A

Williams syndrome, CF

133
Q

chromosome 9

A

Friedreich ataxia

134
Q

chromosome 11

A

Wilms tumor, beta-globin gene defects (SCD, b-thalassemia, MEN1)

135
Q

chromosome 13

A

Patau, Wilson Disease, retinoblastoma (RB1), BRCA2

136
Q

chromosome 15

A

Prader Willi, Angelman, Marfan

137
Q

chromosome 16

A

ADPKD (PKD1), alpha-globin gene defects (a-thalassemia)

138
Q

chromosome 17

A

NF type 1, BRCA1, p53

139
Q

chromosome 18

A

Edward syndrome

140
Q

chromosome 22

A

NF type 2, DiGeorge

141
Q

chromosome X

A

Fragile X, X-linked agammaglobulinemia, Klinefelter syndrome

142
Q

when the long arms of 2 acrocentric chromosomes fuse at the centromere and the 2 short arms are lost - what is this called and what chromosome pairs are normally invovled?

A

Robertsonian translocation

13, 14, 15, 21, 22

143
Q

congenital microdeletion of long arm chromosome 7 (deleted region includes elastin gene)

A

Williams syndrome

144
Q

DiGeorge presentation can be due to

A

aberrant development of 3rd and 4th branchial pouches

145
Q

What vitamin is important for differentiation of epithelial cells into specialized tissue (pancreatic cells, mucus-secreting cells)?

A

vitamin A (retinol)

146
Q

tx for acute promyelocytic leukemia

A

all-trans retinoic acid

147
Q

what happens in Vit A deficiency?

A

night blindness, dry scaly skin, corneal degeneration, bitot spots on conjunctiva, immunosuppression

148
Q

What reactions is thiamine (thiamine pyrophosphate) a cofactor for?

A
  • pyruvate dehydrogenase (links glycolysis to TCA cycle)
  • alpha-ketoglutarate dehydrogenase (TCA cycle)
  • transketolase (HMP Shunt)
  • branched-chain ketoacid dehydrogenase
149
Q

How do you dx vit B1 deficiency?

A

dx made by increase in RBC transketolase activity following Vit B1 administration

150
Q

component of flavins FAD and FMN, used in cofactors in redox reactions, eg the succinate dehydrogenase reaction in TCA cycle

A

Vit B2/riboflavin

151
Q

deficiency of vit B2 presents as

A

cheilosis and corneal vascularization

152
Q

used to tx dyslipidemia; lowers VLDL and raises HDL

what is this derived from?

A

B3/niacin

tryptophan

153
Q

autosomal recessive deficiency of neutral amino acid transporters in proximal renal tubular cells and on enterocytes

A

hartnup disease

154
Q

essential component of CoA, a cofactor for acyl transfers, and fatty acid synthase

A

Vit B5 (pantothenic acid)

155
Q

responsible for synthesis of cystathionine, heme, niacin, histamine, and neurotransmitters including serotonin, epi, NE, DA, and GABA

A

Vit B6 pyridoxine

156
Q

deficiency of vit B6 will cause

A

convulsions, hyperirritability, peripheral neuropathy, sideroblastic anemias due to impaired hemoglobin synthesis and iron excess

157
Q

Vit B7/biotin is a cofactor for carboxylation enzymes in what reactions?

A
  • pyruvate carboxylase
    • pyruvate to oxaloacetate
  • acetyl-CoA carboxylase
    • acetyl CoA to malonyl CoA
  • propionyl CoA carboxylase
    • propionyl CoA to methylmalonyl CoA
158
Q

Where is vit B9 absorbed?

Labs with B9 deficiency show…

A

absorbed in jejunum

increased homocysteine, normal methylmalonic acid levels

159
Q

folate deficiency can be caused by what drugs?

A

phenytoin, sulfonamides, methotrexate

160
Q

what is a cofactor for methionine synthesis?

A

cobalamin (Vit B12)

161
Q

What is the CNS damage a/w B12 deficiency?

A

paresthesias and subacute combined degeneration (degeneration of dorsal columns, lateral corticospinal tracts, and spinocerebellar tracts) due to abnormal myelin

162
Q

Labs a/w B12/cobalamin deficiency?

A

increased serum homocysteine and methylmalonic acid levels, and secondary folate deficiency

163
Q

What does Vit C do?

A
  • antioxidant
  • facilitates iron absorption by reducing it to Fe2+ state
  • necessary for hydroxylation of proline and lysine in collagen synthesis
  • necessary for dopamine beta-hydroxylase, which converts dopamine to NE
164
Q

What vitamin should purely breastfed infants also get?

165
Q

increase activation of Vit D by epithelioid macrophages is seen in what disease?

A

granulomatous disease

166
Q

What is the name for vit E?

A

tocopherol/tocotrienol

167
Q

Vit E deficiency will present with?

A
  • hemolytic anemia
  • acanthocytosis
  • muscle weakness
  • posterior column and spinocerebellar tract demyelination
168
Q

how can you differentiate deficiency of B12 from Vit E when they both have neuro ssx’;

A

E deficiency wont have megaloblastic anemia, hypersegmented neutrophils, or increased serum methylmalonic acid levels

169
Q

high dose supplementation of vit E may alter

A

metabolism of vit K - causing enhanced anticoagulant effects of warfarin

170
Q

What are the names for vitamin K?

A

phytomenadione, phylloquinone, phytonadione

171
Q

deficiency of vit K will present with

A

neonatal hemorrhage with increased PT and aPTT but normal bleeding time (neonates have sterile intestines and are unable to synthesize vit K)

172
Q

zinc deficiency presents with

A
  • delayed wound healing, hypogonadism, decreased adult hair, dysgeusia, anosmia, acrodermatitis enteropathica
173
Q

What is the difference between Kwashiorkor and marasmus?

A
  • Kwashiorkor
    • protein malnutrition
    • skin lesions, edema due to decreased oncotic pressure, liver malfunction (fatty change d/t decrease apolipoprotein synthesis
  • Marasmus
    • malnutrition not causing edema
    • deficient calories but no nutrients are entirely absent
    • muscle wasting
174
Q

What is the limiting reagent in ethanol metabolism?

Alcohol dehydrogenase operates with what order of kinetics?

A

NAD+

zero order kinetics

175
Q

ethanol metabolism increases NADH/NAD+ ratio in the liver causing what to happen?

A
  • pyruvate to lactate
    • lactic acidosis
  • oxaloacetate to malate
    • prevents gluconeogenesis leading to fasting hypoglycemia
  • dihydroxyacetone phosphate to glycerol-3-phosphate
    • combines with fatty acids to make triglycerides leading to hepatosteatosis

chronic alcoholism

176
Q

What metabolic pathways happen both in the mitochondria and the cytosol?

A
  • heme synthesis
  • urea cycle
  • gluconeogenesis

(HUGs take two)

177
Q

What metabolic pathways happen in the mitochondria?

A
  • fatty acid oxidation (beta ox)
  • acetyl-CoA production
  • TCA cycle
  • oxidative phosphorylation
  • ketogenesis
178
Q

rate determining enzymes of glycolysis, gluconeogenesis, TCA cycle, glycogenesis, glycogenolysis

A
  • glycolysis - PFK1
  • gluconeogenesis - fructose-1,6-bisphosphatase
  • TCA cycle - isocitrate dehydrogenase
  • glycogenesis - glycogen synthase
  • glycogenolysis - glycogen phosphorylase
179
Q

ATP production is most efficient aerobically with what shuttles?

A

32 net ATP via malate-asparate shuttle (heart and liver)

30 net ATP via glycerol-3-phosphate shuttle (muscle)

180
Q

What are universal electron acceptors? are they used in catabolic or anabolic processes?

A

Nicotinamides (NAD+ from vit B3, NADP+) and flavin nucleotides (FAD+ from B2)

NAD+ is usually in catabolic processes and NADPH is used in anabolic processes (steroid and FA synthesis)

181
Q

NADPH is a product of what metabolic pathway and is used for…

A

HMP shunt

  • used for
    • anabolic processes
    • respiratory burst
    • cytochrome P450
    • glutathione reductase
182
Q

What is the difference between hexokinase and glucokinase?

A
  • hexokinase
    • most tissues, except liver and pancreatic beta cells
    • not induced by insulin
    • feedback inhibited by Glucose-6-phosphate
  • glucokinase
    • liver and beta cells
    • induced by insulin
    • no feedback inhibited by glucose-6-phosphate
183
Q

regulation by fructose-2,6-bisphosphate in the fasting state

A
  • increased glucagon
    • increases cAMP
      • increases PKA
        • increases FBPase2 and decreases PFK2
          • less glycolysis
            • more gluconeogenesis
184
Q

regulation by fructose-2,6-bisphosphate in the fed state

A
  • increased insulin
    • decreases cAMP
      • decreases PKA
        • decreases FBPase2 and increases PFK2
          • more glycolysis
            • less gluconeogenesis
185
Q

what is the mitochondrial enzyme complex linking glycolysis and TCA cycle?

When is it active?

A

pyruvate dehydrogenase complex

active in fed state

186
Q

The 3 enzymes in the pyruvate dehydrogenase complex require what 5 cofactors?

A
  1. Thiamine pyrophosphate (B1)
  2. lipoic acid
  3. CoA (B5, pantothenic acid)
  4. FAD (B2 riboflavin)
  5. NAD+ (B3 niacin)
187
Q

vomiting, rice-water stools, garlic breath, QT prolongation - poisoned by what?

A

arsenic poisoning

inhibits lipoic acid

188
Q

what results if there is a deficiency in pyruvate dehydrogenase pathway?

A

buildup of pyruvate that gets shunted to lactate (via LDH) and alanine (via ALT)

neuro deficits, lactic acidosis, increased serum alanine starting in infancy

189
Q

what complex requires the same 5 cofactors as the pyruvate dehydrogenase complex?

A

alpha-ketoglutarate dehydrogenase complex

190
Q

What are the products of the TCA cycle?

A

3 NADH, 1 FADH2, 2 CO2, 1 GTP per acetyl-CoA = 10 ATP/acetyl-CoA

(2x everything per glucose)

191
Q

NADH electrons from glycolysis enter mitochondria via

A

the malate-aspartate or glycerol-3-phosphate shuttle

192
Q

What substances directly inhibit electron transport? Where do they act?

A
  • rotenone - complex I inhibitor
  • antimycin A - complex III inhibitor
  • CO, cyanide - complex IV inhibitor
193
Q

What is an ATP synthase inhibitor? what happens?

A

oligomycin

directly inhibits mitochondrial ATP synthase, causing an increased proton gradient

no ATP produced

194
Q

What agents do uncoupling of the ETC, increasing permeability, causing a decreased proton gradient and increased O2 consumption?

What else does this do?

A

2,4-dinitrophenol (used illicityly for wt loss)

aspirin (fevers occur s/p OD)

thermogenin in brown fat

ATP synthesis stops, but ETC continues; produces heat

195
Q

What are the irreversible enzymes in gluconeogenesis?

A
  • pyruvate carboxylase
  • phosphoenolpyruvate carboxykinase
  • fructose-1,6-bisphosphatase
  • glucose-6-phosphatase
196
Q

essential fructosuria is a benign condition with what defect?

A

defect in fructokinase

197
Q

hereditary deficiency of aldolase B

A

fructose intolerance

198
Q

symptoms following consumption of fruit, juice or honey, presenting with hypoglycemia, jaundice, cirrhosis, and vomiting

dx?

tx?

A

fructose intolerance

decrease intake of both fructose and sucrose (glucose+fructose)

199
Q

What metabolic pathways are inhibited in fructose intolerance?

A

glycogenolysis and gluconeogenesis

200
Q

galactose is appearing in blood and urine; infantile cataracts; may present as failure to track objects or to develop a social smile

dx?

what accumulates?

A

galactokinase deficiency

galactitol accumulates if galactose is present in diet; mild condition

201
Q

in Classic Galactosemia there is an absence of …

this causes damge by…

can predispose to what…

A

galactose-1-phosphate uridyltransferase

accumulation of toxic substances (including galactitol which accumulates in the lens of the eye)

E. coli sepsis in neonates

202
Q

What enzyme changes glucose to sorbitol?

Sorbitol can accumulate if there is not this enzyme in the tissues..

What tissues don’t have this enzyme?

A

aldose reductase

sorbitol dehydrogenase (converts to fructose)

lens (mix), retina, kidneys, and schwann cells have only aldose reductase

203
Q

What does stool and breath show with lactase deficiency?

A

stool shows decreased pH and breath shows increased H+ content with lactose hydrogen breath test

204
Q

What are the basic amino acids?

A

His, lys, arg

Arg most basic

His has no charge at body pH

205
Q

What are the glucogenic amino acids?

A

methionine, histidine, and valine

206
Q

What does the urea cycle do?

A

excess nitrogen is converted to urea and excreted by the kidneys

207
Q

urea cycle steps/enzymes

A
  • N-acetylglutamate is the allosteric activator of carbamoyl phosphate synthetase I
    • creates carbamoyl phosphate
      • ornithine transcarbamylase
    • citrulline
      • argininosuccinate synthetase plus Aspartate and ATP
    • argininosuccinate
      • argininosuccinase
    • arginine (and fumarate goes away)
      • arginase and water
    • urea to kidney and ornithine back to cycle
208
Q

hyperammonemia results in what substances being depleted?

A

excess NH3, depleting alpha-ketoglutarate, leading to inhibition of TCA cycle

209
Q

what is the MC urea cycle disorder?

what happens?

A

ornithine transcarbamylase deficiency - X linked recessive (other urea cycle issues are autosomal recessive)

excess carbamoyl phosphate is converted to orotic acid (part of pyrimidine synthesis pathway)

210
Q

increased orotic acid in blood and urine would lead me to think of…

what else do I see on labs?

A

ornithine transcarbamylase deficiency

also find decreased BUN, symptoms of hyperammonemia; no megaloblastic anemia (v orotic aciduria)

211
Q

PKU is due to…

A

decreased phenylalanine hydroxylase or decreased tetrahydrobiopterin (BH4) cofactor

212
Q

tx of PKU

A

decrease phenylalanine and increase tyrosine in diet, tetrahydrobiopterin supplementation

213
Q

blocked degradation of branched amino acids (isoleucine, leucine, valine) due to decreased branched-chain alpha-katoacid dehydrogenase

dx and tx

A

maple syrup urine disease

restriction of leucine, isoleucine, and valine in diet, supplement with thiamine

214
Q

congenital deficiency of homogentisate oxidase in the degradative pathway of tyrosine to fumarate

dx?

what does this cause?

A

alkaptonuria

pigment-forming homogentisic acid accumulates in tissue

usually benign - bluish black CT, ear cartilage, and sclerae; urine turns black on prolonged exposure to air; may have debilitating arthralgias

215
Q

What do all of these cause? - cystathionine synthase deficiency; decreased affinity of cystathionine synthase for pyridoxal phosphate; methionine synthase deficiency

A

homocystinuria

  • increase homocysteine in urine
  • osteoporosis
  • marfanoid habitus
  • ocular changes
  • cardiovascular effects
  • kyphosis
  • intellectual disability
216
Q

What is the diagnostic test for cystinuria?

A

urinary cyanide-nitroprusside test

217
Q

cystinuria is a hereditary defect of renal PCT and intestinal aa transporter that prevents reabsorption of…

what shape are cystine stones?

A

cystine, ornithine, lysine, and arginine

hexagonal

218
Q

tx of cystinuria?

A

urinary alkalinization (K+ citrate, acetozolamide) and chelating agents (penicillamine) increase solubility of cystine stones; good hydration

219
Q

What is the deficient enzyme and what is accumulated in Tay Sachs?

A

deficient: hexosaminidase A

accumulate GM2 ganglioside

220
Q

What is the deficient enzyme and what is accumulated in Fabry disease?

A

deficient alpha-galactosidase A

accumulate ceramide trihexoside

221
Q

What is the deficient enzyme and what is accumulated in metachromatic leukodystrophy?

A

deficient arylsulfatase A

accumulate cerebroside sulfate

222
Q

What is the deficient enzyme and what is accumulated in Krabbe disease?

A

deficient galactocerebrosidase

accumulate galactocerebroside, psychosine

223
Q

What is the deficient enzyme and what is accumulated in Gaucher disease?

A

deficient in glucocerebrosidase (beta-glucosidase)

accumulate glucocerebroside

224
Q

hepatosplenomegaly, pancytopenia, osteoporosis, avascular necrosis of the femur, bone crises, and lipid laden macrophages resembling crumpled tissue paper

A

Gaucher disease

225
Q

What is the deficient enzyme and what is accumulated in Niemann-Pick disease?

A

deficient sphingomyelinase

accumulate sphingomyelin

226
Q

DD, gargoylism, airway obstruction, corneal clouding, hepatosplenomegaly

dx?

what is deficient and what accumulates?

A

Hurler syndrome

deficient alpha-L-iduronidase

accumulate heparan sulfate and dermatan sulfate

227
Q

Mild hurler syndrome plus aggressive behavior and no corneal clouding

A

Hunter syndrome

deficient iduronate sulfatase

accumulate heparan sulfate and dermatan sulfate

228
Q

What shuttles are used in fatty acid metabolism?

A

citrate shuttle in fatty acid synthesis

carnitine shuttle in fatty acid degradation

229
Q

degradation of TGs circulating in chylomicrons and VLDLs; found on vascular endothelial surface

A

lipoprotein lipase (LPL)

230
Q

degradation of TGs remaining in IDL

A

hepatic TG lipase

231
Q

what catalyzes esterification of 2/3 of plasma cholesterol

232
Q

How is LDL taken up?

A

taken up by target cells via receptor-mediated endocytosis

233
Q

HDL acts as a repository for

A

apolipoproteins C and E

234
Q

AR, chylomicrons, LDL, and VLDL absent; deficiency in apoB48 and apoB100

A

abetalipoproteinemia

235
Q

lipoprotein lipase or apoCII deficiency

dx

what will be in blood?

A

Type I familial dyslipidemia - hyperchylomicronemia

chylomicrons, TG, cholesterol increased

236
Q

defective apoE and increased chylomicrons and VLDL in blood

A

Dysbetalipoproteinemia/Type III

237
Q

hepatic overproduction of VLDL

A

hypertriglyceridemia (type IV)

Board questions (24 decks)

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